P05042 (FUMC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Fumarate hydratase class II
Short name=Fumarase C
EC=4.2.1.2

Alternative name(s):
Iron-independent fumarase

Gene names

Name:	fumC
Ordered Locus Names:	b1611, JW1603

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	467 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible addition of water to fumarate to give L-malate. Ref.7
Catalytic activity	(S)-malate = fumarate + H2O. Ref.7
Enzyme regulation	Inhibited by ATP and S-2,3-dicarboxyaziridine. Ref.7
Pathway	Carbohydrate metabolism; tricarboxylic acid cycle; (S)-malate from fumarate: step 1/1. HAMAP-Rule MF_00743
Subunit structure	Homotetramer. Ref.7 Ref.8 Ref.9 Ref.14 Ref.16
Subcellular location	Cytoplasm HAMAP-Rule MF_00743.
Induction	Under conditions of iron limitation and oxidative stress. Ref.7 Ref.10
Miscellaneous	There are 2 substrate binding sites: the catalytic A site, and the non-catalytic B site that may play a role in the transfer of substrate or product between the active site and the solvent. Alternatively, the B site may bind allosteric effectors. HAMAP-Rule MF_00743
Sequence similarities	Belongs to the class-II fumarase/aspartase family. Fumarase subfamily.
Biophysicochemical properties	Kinetic parameters: KM=50 µM for L-malate (at pH 7.3 and 30 degrees Celsius) Ref.7 pH dependence: Optimum pH is 8.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Cellular component	Cytoplasm
Molecular function	Lyase
Technical term	3D-structure Allosteric enzyme Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	fumarate metabolic process Inferred from electronic annotation. Source: InterPro response to oxidative stress Inferred from expression pattern PubMed 1631070. Source: EcoCyc tricarboxylic acid cycle Inferred from electronic annotation. Source: HAMAP
Cellular_component	tricarboxylic acid cycle enzyme complex Inferred from electronic annotation. Source: InterPro
Molecular_function	fumarate hydratase activity Inferred from direct assay Ref.8. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 467

467

Fumarate hydratase class II HAMAP-Rule MF_00743

PRO_0000161275

Regions

Region

98 – 100

3

Substrate binding HAMAP-Rule MF_00743

Region

129 – 132

4

B site HAMAP-Rule MF_00743

Region

139 – 141

3

Substrate binding HAMAP-Rule MF_00743

Region

187 – 188

2

Substrate binding By similarity

Region

324 – 326

3

Substrate binding By similarity

Sites

Active site

188

1

Proton donor/acceptor By similarity

Active site

318

1

By similarity

Binding site

319

1

Substrate By similarity

Site

331

1

Important for catalytic activity

Experimental info

Mutagenesis

126

1

R → A: Reduces enzyme activity 10-fold. Ref.12

Mutagenesis

127

1

K → D: No effect. Ref.12

Mutagenesis

129

1

H → N: No effect on activity, but the carboxyamide group from Asn129 swings into the B site and replaces S-malate by forming a bifurcated hydrogen bond with Asn131 and Asp132. Ref.12 Ref.15

Mutagenesis

188

1

H → N: Reduces activity 200-fold. Ref.15

Mutagenesis

315

1

E → Q: Reduces activity 10-fold. Ref.16

Secondary structure

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467

Helix Strand Turn

Details...

Beta strand

5 – 9

5

Beta strand

12 – 16

5

Helix

24 – 32

9

Helix

42 – 61

20

Helix

67 – 81

15

Turn

82 – 85

4

Helix

86 – 88

3

Beta strand

92 – 95

4

Helix

100 – 117

18

Helix

130 – 134

5

Turn

135 – 137

3

Helix

140 – 158

19

Helix

160 – 177

18

Turn

178 – 180

3

Beta strand

182 – 187

6

Beta strand

190 – 196

7

Helix

197 – 222

26

Turn

230 – 232

3

Helix

242 – 254

13

Helix

264 – 269

6

Helix

272 – 298

27

Beta strand

302 – 305

4

Beta strand

308 – 310

3

Helix

328 – 352

25

Helix

362 – 386

25

Helix

388 – 390

3

Helix

395 – 404

10

Helix

406 – 408

3

Helix

409 – 413

5

Turn

414 – 416

3

Helix

418 – 431

14

Helix

435 – 441

7

Helix

447 – 453

7

Helix

456 – 458

3

Sequences

	Sequence		Length	Mass (Da)
	P05042 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 3D67E3C0F0FDF40B	FASTA	467	50,489
	10 20 30 40 50 60 MNTVRSEKDS MGAIDVPADK LWGAQTQRSL EHFRISTEKM PTSLIHALAL TKRAAAKVNE 70 80 90 100 110 120 DLGLLSEEKA SAIRQAADEV LAGQHDDEFP LAIWQTGSGT QSNMNMNEVL ANRASELLGG 130 140 150 160 170 180 VRGMERKVHP NDDVNKSQSS NDVFPTAMHV AALLALRKQL IPQLKTLTQT LNEKSRAFAD 190 200 210 220 230 240 IVKIGRTHLQ DATPLTLGQE ISGWVAMLEH NLKHIEYSLP HVAELALGGT AVGTGLNTHP 250 260 270 280 290 300 EYARRVADEL AVITCAPFVT APNKFEALAT CDALVQAHGA LKGLAASLMK IANDVRWLAS 310 320 330 340 350 360 GPRCGIGEIS IPENEPGSSI MPGKVNPTQC EALTMLCCQV MGNDVAINMG GASGNFELNV 370 380 390 400 410 420 FRPMVIHNFL QSVRLLADGM ESFNKHCAVG IEPNRERINQ LLNESLMLVT ALNTHIGYDK 430 440 450 460 AAEIAKKAHK EGLTLKAAAL ALGYLSEAEF DSWVRPEQMV GSMKAGR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structural and functional relationships between fumarase and aspartase. Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12." Woods S.A., Miles J.S., Roberts R.E., Guest J.R. Biochem. J. 237:547-557(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Complete nucleotide sequence of the fumarase gene fumA, of Escherichia coli." Miles J.S., Guest J.R. Nucleic Acids Res. 12:3631-3642(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-89.
[6]	"The fumarase genes of Escherichia coli: location of the fumB gene and discovery of a new gene (fumC)." Guest J.R., Miles J.S., Roberts R.E., Woods S.A. J. Gen. Microbiol. 131:2971-2984(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-89.
[7]	"Purification and characterization of two types of fumarase from Escherichia coli." Ueda Y., Yumoto N., Tokushige M., Fukui K., Ohya-Nishiguchi H. J. Biochem. 109:728-733(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-20, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.
[8]	"Purification and crystallization of fumarase C from Escherichia coli." Weaver T.M., Levitt D.G., Banaszak L.J. J. Mol. Biol. 231:141-144(1993) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15, SUBUNIT.
[9]	"Two biochemically distinct classes of fumarase in Escherichia coli." Woods S.A., Shwartzbach S.D., Guest J.R. Biochim. Biophys. Acta 954:14-26(1988) [PubMed] [Europe PMC] [Abstract] Cited for: BIOCHEMICAL ANALYSIS OF FUMA AND FUMC, SUBUNIT.
[10]	"Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products." Park S.J., Gunsalus R.P. J. Bacteriol. 177:6255-6262(1995) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[11]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[12]	"The role of the allosteric B site in the fumarase reaction." Rose I.A., Weaver T.M. Proc. Natl. Acad. Sci. U.S.A. 101:3393-3397(2004) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-126; LYS-127 AND HIS-129.
[13]	"Aspartase/fumarase superfamily: a common catalytic strategy involving general base-catalyzed formation of a highly stabilized aci-carboxylate intermediate." Puthan Veetil V., Fibriansah G., Raj H., Thunnissen A.M., Poelarends G.J. Biochemistry 51:4237-4243(2012) [PubMed] [Europe PMC] [Abstract] Cited for: REACTION MECHANISM.
[14]	"Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli." Weaver T., Banaszak L. Biochemistry 35:13955-13965(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), SUBUNIT.
[15]	"Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site." Weaver T., Lees M., Banaszak L. Protein Sci. 6:834-842(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF MUTANTS ASN-129 AND ASN-188 IN COMPLEX WITH MALATE AND CITRATE, MUTAGENESIS OF HIS-129 AND HIS-188.
[16]	"X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation." Estevez M., Skarda J., Spencer J., Banaszak L., Weaver T.M. Protein Sci. 11:1552-1557(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF MUTANT GLN-315, MUTAGENESIS OF GLU-315, SUBUNIT.
[17]	"Structure of free fumarase C from Escherichia coli." Weaver T. Acta Crystallogr. D 61:1395-1401(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X04065 Genomic DNA. Translation: CAA27698.1.
U00096 Genomic DNA. Translation: AAC74683.1.
AP009048 Genomic DNA. Translation: BAA15349.1.
X00522 Genomic DNA. Translation: CAA25205.1.

PIR

UFEC. S07138.

RefSeq

NP_416128.1. NC_000913.2.
YP_489874.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FUO	X-ray	1.98	A/B	1-467	[»]
1FUP	X-ray	2.30	A/B	1-467	[»]
1FUQ	X-ray	2.00	A/B	1-467	[»]
1FUR	X-ray	1.95	A/B	1-467	[»]
1KQ7	X-ray	2.60	A/B	1-467	[»]
1YFE	X-ray	2.19	A	1-467	[»]
2FUS	X-ray	2.20	A/B	1-467	[»]

ProteinModelPortal

P05042.

SMR

P05042. Positions 4-459.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9719N.

IntAct

P05042. 14 interactions.

STRING

511145.b1611.

Proteomic databases

PaxDb

P05042.

PRIDE

P05042.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74683; AAC74683; b1611.
BAA15349; BAA15349; BAA15349.

GeneID

12934129.
946147.

KEGG

ecj:Y75_p1587.
eco:b1611.

PATRIC

32118524. VBIEscCol129921_1682.

Organism-specific databases

EchoBASE

EB0353.

EcoGene

EG10358. fumC.

Phylogenomic databases

eggNOG

COG0114.

HOGENOM

HOG000061736.

KO

K01679.

OMA

KDTMGEV.

ProtClustDB

PRK00485.

Enzyme and pathway databases

BioCyc

EcoCyc:FUMC-MONOMER.
ECOL316407:JW1603-MONOMER.
MetaCyc:FUMC-MONOMER.

SABIO-RK

P05042.

UniPathway

UPA00223; UER01007.

Gene expression databases

Genevestigator

P05042.

Family and domain databases

Gene3D

1.10.275.10. 1 hit.

HAMAP

MF_00743. FumaraseC.

InterPro

IPR005677. Fum_hydII.
IPR024083. Fumarase/histidase_N.
IPR018951. Fumarase_C_C.
IPR000362. Fumarate_lyase.
IPR020557. Fumarate_lyase_CS.
IPR022761. Fumarate_lyase_N.
IPR008948. L-Aspartase-like.
[Graphical view]

Pfam

PF10415. FumaraseC_C. 1 hit.
PF00206. Lyase_1. 1 hit.
[Graphical view]

PRINTS

PR00149. FUMRATELYASE.

SUPFAM

SSF48557. L-Aspartase-like. 1 hit.

TIGRFAMs

TIGR00979. fumC_II. 1 hit.

PROSITE

PS00163. FUMARATE_LYASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P05042.

Entry information

Entry name

FUMC_ECOLI

Accession

Primary (citable) accession number: P05042
Secondary accession number(s): P76891

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	May 1, 2013
This is version 139 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program